The Apple Genome and Epigenome

A Project Led by the Bucher Lab

Welcome to our high quality apple genome and methylome

Using a homozygous apple variety (a doubled haploid of ‘Golden Delicious’) and by combining several of the latest sequencing and mapping technologies, we have obtained a very high quality genome. This allowed us to also better map the “dark matter” of the apple genome, which is rich in transposable elements (57% of the genome). The genome has been published in Nature Genetics.

The apple genome will regularly be updated and you will find all the information on this website.

If you have any suggestions (e.g. corrections in gene annotation), please let us know!

Comments are most welcome: drop an email to

Visit the apple genome 

Our genome bowser contains a wealth of information:

  • Up to date gene annotation
  • Transposable element annotation
  • Genetic markers
  • DNA methylation data
  • small RNA data
  • Microarray probes

New information will be added on are regular bases


Genome sequencing is not a trivial task and is often limited by the quality of the extracted DNA. To help you with your sequencing projects we provide detailed DNA extraction protocols. You can find them in our protocols section.



The raw sequence data and annotation files can be found in the downloads section.



High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. 

Nicolas Daccord, Jean Marc Celton, Gareth Linsmith, Claude Becker, Nathalie Choisne, Elio Schijlen, Henri van de Geest, Luca Bianco, Diego Micheletti, Riccardo Velasco, Erica Adele Di Pierro, Jerome Gouzy, D Jasper G Rees, Philippe Guérif, Hélène Muranty, Charles-Eric Durel, François Laurens, Yves Lespinasse, Sylvain Gaillard, Sébastien Aubourg, Hadi Quesneville, Detlef Weigel, Eric Van de Weg, Michela Troggio, and Etienne Bucher.

Nat Genet, 2017

Yes, the apple  genome has its own Twitter account! Follow it to get genome updates: @AppleGenome

An actual image of the apple genome obtained by BioNano optical mapping.

ⓒ Henry van de Geest

by the Bucher laboratory